title: ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.
abstract: High content studies that profile mouse and human embryonic stem cells (m/hESCs) using various genome-wide technologies such as transcriptomics and proteomics are constantly being published. However, efforts to integrate such data to obtain a global view of the molecular circuitry in m/hESCs are lagging behind. Here, we present an m/hESC-centered database called Embryonic Stem Cell Atlas from Pluripotency Evidence integrating data from many recent diverse high-throughput studies including chromatin immunoprecipitation followed by deep sequencing, genome-wide inhibitory RNA screens, gene expression microarrays or RNA-seq after knockdown (KD) or overexpression of critical factors, immunoprecipitation followed by mass spectrometry proteomics and phosphoproteomics. The database provides web-based interactive search and visualization tools that can be used to build subnetworks and to identify known and novel regulatory interactions across various regulatory layers. The web-interface also includes tools to predict the effects of combinatorial KDs by additive effects controlled by sliders, or through simulation software implemented in MATLAB. Overall, the Embryonic Stem Cell Atlas from Pluripotency Evidence database is a comprehensive resource for the stem cell systems biology community. Database URL: http://www.maayanlab.net/ESCAPE
authors.affiliation: Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1215, New York, NY 10029, USA.
authors.forename: Huilei
authors.initials: H
authors.lastname: Xu
authors.forename: Caroline
authors.initials: C
authors.lastname: Baroukh
authors.forename: Ruth
authors.initials: R
authors.lastname: Dannenfelser
authors.forename: Edward Y
authors.initials: EY
authors.lastname: Chen
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Tan
authors.forename: Yan
authors.initials: Y
authors.lastname: Kou
authors.forename: Yujin E
authors.initials: YE
authors.lastname: Kim
authors.forename: Ihor R
authors.initials: IR
authors.lastname: Lemischka
authors.forename: Avi
authors.initials: A
authors.lastname: Ma'ayan
mesh_terms: D000818:Animals; D015415:Biomarkers / Q000378:metabolism; D019070:Cell Lineage; D019992:Databases as Topic; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D057166:High-Throughput Screening Assays; D006801:Humans; D051379:Mice; D039904:Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism; D011642:Publications; D057386:Search Engine
chemical_list: D015415:Biomarkers